Strain identifier
BacDive ID: 3030
Type strain: 
Species: Pseudorhodoferax soli
Strain Designation: TBEA3
Strain history: <- N. Bruland, Univ. Münster, Inst. Mol. Microbiol. Biotechnol., Germany; TBEA3
NCBI tax ID(s): 545864 (species)
version 9.2 (current version)
General
@ref: 15850
BacDive-ID: 3030
DSM-Number: 21634
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Pseudorhodoferax soli TBEA3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil sample.
NCBI tax id
- NCBI tax id: 545864
- Matching level: species
strain history
- @ref: 15850
- history: <- N. Bruland, Univ. Münster, Inst. Mol. Microbiol. Biotechnol., Germany; TBEA3
doi: 10.13145/bacdive3030.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Pseudorhodoferax
- species: Pseudorhodoferax soli
- full scientific name: Pseudorhodoferax soli Bruland et al. 2009
@ref: 15850
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Pseudorhodoferax
species: Pseudorhodoferax soli
full scientific name: Pseudorhodoferax soli Bruland et al. 2009
strain designation: TBEA3
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29123 | negative | 1.95 µm | 0.85 µm | rod-shaped | yes | |
| 69480 | negative | 98.486 |
Culture and growth conditions
culture medium
- @ref: 15850
- name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 15850 | positive | growth | 28 |
| 29123 | positive | optimum | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 29123
- oxygen tolerance: aerobe
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29123 | 30089 | acetate | + | carbon source |
| 29123 | 17128 | adipate | + | carbon source |
| 29123 | 22599 | arabinose | + | carbon source |
| 29123 | 28757 | fructose | + | carbon source |
| 29123 | 24265 | gluconate | + | carbon source |
| 29123 | 25115 | malate | + | carbon source |
| 29123 | 29864 | mannitol | + | carbon source |
| 29123 | 17272 | propionate | + | carbon source |
| 29123 | 30031 | succinate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29123 | catalase | + | 1.11.1.6 |
| 29123 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 15850
- sample type: soil sample
- geographic location: Marschacht near Hamburg
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_2008.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_1115;97_1307;98_1572;99_2008&stattab=map
- Last taxonomy: Pseudorhodoferax
- 16S sequence: EU825700
- Sequence Identity:
- Total samples: 934
- soil counts: 76
- aquatic counts: 712
- animal counts: 127
- plant counts: 19
Safety information
risk assessment
- @ref: 15850
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15850
- description: Pseudorhodoferax soli strain TBEA3 16S ribosomal RNA gene, partial sequence
- accession: EU825700
- length: 1524
- database: nuccore
- NCBI tax ID: 545864
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudorhodoferax soli DSM 21634 | GCA_003337555 | scaffold | ncbi | 545864 |
| 66792 | Pseudorhodoferax soli strain DSM 21634 | 545864.3 | wgs | patric | 545864 |
| 66792 | Pseudorhodoferax soli DSM 21634 | 2770939619 | draft | img | 545864 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 15850 | 69.1 | high performance liquid chromatography (HPLC) |
| 29123 | 69.1 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.486 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.71 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.357 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 82.74 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 82.794 | no |
External links
@ref: 15850
culture collection no.: DSM 21634, LMG 24555
straininfo link
- @ref: 72550
- straininfo: 358705
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19625429 | Pseudorhodoferax soli gen. nov., sp. nov. and Pseudorhodoferax caeni sp. nov., two members of the class Betaproteobacteria belonging to the family Comamonadaceae. | Bruland N, Bathe S, Willems A, Steinbuchel A | Int J Syst Evol Microbiol | 10.1099/ijs.0.006791-0 | 2009 | Betaproteobacteria/classification/genetics/isolation & purification/metabolism, Comamonadaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Metabolism |
| Phylogeny | 22368172 | Pseudorhodoferax aquiterrae sp. nov., isolated from groundwater. | Chen WM, Lin YS, Young CC, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijs.0.039842-0 | 2012 | Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Groundwater/*microbiology, Hydroxybutyrates/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, Polyesters/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, *Water Microbiology | Genetics |
| Phylogeny | 25212224 | Comamonas humi sp. nov., isolated from soil. | Hatayama K | Int J Syst Evol Microbiol | 10.1099/ijs.0.067439-0 | 2014 | Bacterial Typing Techniques, Base Composition, Comamonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15850 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21634) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21634 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 29123 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25549 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 72550 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID358705.1 | StrainInfo: A central database for resolving microbial strain identifiers |